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Microsatellite analysis was used to examine intraspecific polymorphism in two extensive continental isolates of the striped field mouse (Apodemus agrarius Pallas, 1771) separated by the Baikal disjunction. Striped field mice from the western isolate (from the European and Kazakh-Siberian parts of the range) and from the eastern isolate (from the territory of the Middle Amur Region and Coastal Territory of Far East) were tested. The analysis used 180 specimens collected from 33 localities and five microsatellite loci developed earlier for the genus Apodemus. The work was carried out based on the summation of local samples in each of the aforementioned geographical regions. It was shown that allelic diversity and the number of specific alleles were higher in the eastern isolate that may be the result of the longer habitation of the striped field mouse in the eastern part of the range. The limited number of specific alleles in the western isolate as compared to the eastern one can be determined by the founder effect and may reflect the direction of the historical migration of the species from east to west. Our results demonstrate no more than a population level of differentiation within the continental isolates of the striped field mouse and indicate no more than a subspecies level of differences between these isolated forms, i.e., the relatively recent penetration of A. agrarius to western Eurasia.